In Aliens, the queen inaudibly commanded her warriors to withdraw after Ripley threatened her eggs. In Alien Resurrection, Ripley said "I can hear them, they're so close" and "it's the queen, she's in pain". These imply that the aliens have a way of communicating inaudibly.
According to the old novels (I don't know which ones since I haven't read them), aliens communicate by telepathy. The novelization of Alien Resurrection also says they're telepathic.
The video game Aliens versus Predator 2 says they communicate by ultrasound. I heard somewhere that an old version of the Alien Resurrection script also suggested this.
The Alien Legacy website says this about the alien queen: "It is believed that she communicates her will through the secretion of pheromones or possibly by an empathic link."
I prefer the ultrasound theory. What do you guys think?